I'am working on a Seven 64Bits and W2K8 R2 for one year now, and, on the command line, I'am always using 64 bits Powershell without any troubles.
For me the problem is not to choose 32 or 64 Bit PowerShell.exe, but to know that the two exists, and that a 32 bits process will use the 32 bits PowerShell. For example if you use PowerShell as post build execution script in Visual Studio 2010, it will use 32 bits PoweShell because Visual Studio 2010 is 32 bits process.
The two versions see two differents places in the registry so you have to Set-ExecutionPolicy for both.
As scripting is concerned I do not use ISE, but PowerGUI script Editor. You can use
[intPtr]::size
in a script to know if you are runing 32 or 64 bits PowerShell.exe.